The consolidation status of a seabed under marine structures and hydrostatic pressure is the basis for the evaluation of the liquefaction and dynamic shear failure of seabed foundation under ocean wave loading. However, only a few investigations have been conducted for the seabed consolidation under hydrostatic pressure and marine structures. Furthermore, most previous numerical models for the Biot's consolidation theory are limited to two-dimensional cases. In this study, based on Biot's dynamic poro-elastic theory ("u-pu-p" approximation), a three-dimensional FEM seabed model is adopted to investigate the consolidation of seabed under a rubble mound breakwater and hydrostatic pressure. Numerical results show that the rubble mound breakwater significantly affect the stress/displacement fields in the seabed foundation. Based on the parametric study, it can be concluded: (1) Young's modulus of a seabed significantly affects the settlement of breakwater; and (2) the magnitude of the shear stress concentrates in the zones beneath the toes of breakwater.